To evaluate the performance of a real valued ge netic algorithm GA exploiting domain knowledge we sys tematically evaluate the e ect of exogenous parameters us ing analysis of variance The GA platform used for this study is Genocop III a real valued co evolutionary algo rithm implementation for numerical optimization We use the protein structure prediction PSP problem as our test domain Nearly ...

The free energies of hydration of the 20 amino acids in their zwitterionic form, their shifts and the side-chain free energies of a transfer have been calculated using the Ðnite di†erence PoissonÈBoltzmann methodology. A comparison of the results obtained with charge and size parameters from some popular force Ðelds used in modelling biomolecules is presented. The force Ðelds considered include...

A good docking algorithm requires an energy function that is selective, in that it clearly differentiates correctly docked structures from misdocked ones, and that is efficient, meaning that a correctly docked structure can be identified quickly. We assess the selectivity and efficiency of a broad spectrum of energy functions, derived from systematic modifications of the CHARMM param19rtoph19 e...

This article describes the application of our distributed computing framework for crystal structure prediction (CSP) the modified genetic algorithms for crystal and cluster prediction (MGAC), to predict the crystal structure of flexible molecules using the general Amber force field (GAFF) and the CHARMM program. The MGAC distributed computing framework includes a series of tightly integrated co...

New sets of parameters (maps) for calculating amide I vibrational spectra for proteins through a vibrational exciton model are proposed. The maps are calculated as a function of electric field and van der Waals forces on the atoms of peptide bonds, taking into account the full interaction between peptide bonds and the surrounding environment. The maps are designed to be employed using data obta...

We present a method called MOPED for optimizing energetic and structural parameters in computational models, including all-atom energy functions, when native structures and decoys are given. The present method goes beyond previous approaches in treating energy functions that are nonlinear in the parameters and continuous in the degrees of freedom. We illustrate the method by improving solvation...